X-79363028-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004867.5(ITM2A):c.355G>A(p.Glu119Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,204,252 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004867.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITM2A | NM_004867.5 | c.355G>A | p.Glu119Lys | missense_variant | 3/6 | ENST00000373298.7 | |
ITM2A | NM_001171581.2 | c.223G>A | p.Glu75Lys | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITM2A | ENST00000373298.7 | c.355G>A | p.Glu119Lys | missense_variant | 3/6 | 1 | NM_004867.5 | P1 | |
ITM2A | ENST00000434584.2 | c.223G>A | p.Glu75Lys | missense_variant | 2/5 | 2 | |||
ITM2A | ENST00000469541.5 | n.315G>A | non_coding_transcript_exon_variant | 3/6 | 2 | ||||
ITM2A | ENST00000482194.1 | n.326G>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000899 AC: 1AN: 111285Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33479
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183045Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67553
GnomAD4 exome AF: 9.15e-7 AC: 1AN: 1092915Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 358421
GnomAD4 genome AF: 0.00000898 AC: 1AN: 111337Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33541
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2022 | The c.355G>A (p.E119K) alteration is located in exon 3 (coding exon 3) of the ITM2A gene. This alteration results from a G to A substitution at nucleotide position 355, causing the glutamic acid (E) at amino acid position 119 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at